Package: CytoSimplex 0.1.99

Yichen Wang

CytoSimplex: Simplex Visualization of Cell Fate Similarity in Single-Cell Data

Create simplex plots to visualize the similarity between single-cells and selected clusters in a 1-/2-/3-simplex space. Velocity information can be added as an additional layer. See Liu J, Wang Y et al (2023) <doi:10.1101/2023.12.07.570655> for more details.

Authors:Yichen Wang [aut, cre], Jialin Liu [aut], Joshua Welch [cph]

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CytoSimplex.pdf |CytoSimplex.html
CytoSimplex/json (API)
NEWS

# Install 'CytoSimplex' in R:
install.packages('CytoSimplex', repos = c('https://welch-lab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/welch-lab/cytosimplex/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • rnaCluster - Major cell type annotation of the example mouse bone marrow data
  • rnaRaw - Mouse bone marrow scRNAseq example data
  • rnaVelo - Velocity graph of the example mouse bone marrow data

On CRAN:

10 exports 1 stars 1.32 score 75 dependencies 160 downloads

Last updated 2 months agofrom:7e89f55494

Exports:colNormalizeplotBinaryplotQuaternaryplotTernaryreadH5ADObsNamesreadH5ADObsVarreadH5ADUnsSpMatreadVelocytoLoomselectTopFeatureswriteQuaternaryGIF

Dependencies:askpassbase64encbslibcachemclicolorspacecpp11crosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemisc3dmunsellnlmeopensslpillarpkgconfigplot3DplotlypromisespurrrR6rappdirsRColorBrewerRcppRcppArmadillorlangrmarkdownsassscalesstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Normalize each column of the input matrix by the column sumcolNormalize colNormalize.default colNormalize.dgCMatrix colNormalize.Seurat colNormalize.SingleCellExperiment
Create binary plotsplotBinary plotBinary.default plotBinary.Seurat plotBinary.simMat plotBinary.SingleCellExperiment
Create quaternary simplex plotsplotQuaternary plotQuaternary.default
Craete quaternary simplex plot with Seurat objectplotQuaternary.Seurat
Create quaternary simplex plot with pre-calculated similarity matrixplotQuaternary.simMat
Create quaternary simplex plot with SingleCellExperiment objectplotQuaternary.SingleCellExperiment
Create ternary simplex plotsplotTernary plotTernary.default
Create ternary simplex plot with Seurat objectsplotTernary.Seurat
Create quaternary simplex plot with pre-calculated similarity matrixplotTernary.simMat
Create ternary simplex plot with SingleCellExperiment objectsplotTernary.SingleCellExperiment
Show plist object produced with plot3D packageprint.quatPlot
Extract `adata.obs_names` from an H5AD filereadH5ADObsNames
Extract a variable from adata.obs stored in an H5AD filereadH5ADObsVar
Extract a sparse matrix from adata.uns stored in an H5AD filereadH5ADUnsSpMat
Extract the raw counts from a LOOM filereadVelocytoLoom
Major cell type annotation of the example mouse bone marrow datarnaCluster
Mouse bone marrow scRNAseq example datarnaRaw
Velocity graph of the example mouse bone marrow datarnaVelo
Pick top differentially presented features for similarity calculationselectTopFeatures selectTopFeatures.default selectTopFeatures.Seurat selectTopFeatures.SingleCellExperiment
Create GIF image for dynamic rotating view of 3D quaternary simplex plotwriteQuaternaryGIF